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Bio 361 - Molecular Genome and Genomics > Midterm 1 - Notes 5 (Part 1) > Flashcards

Midterm 1 - Notes 5 (Part 1) Flashcards

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Biology 101 flashcards
1
Q

If you have a SNP what does it tell you?

A

That you have increase likelihood that you will get a certain type of disease, not that you will actually get it

  • they are not predictors
  • the linkages are pretty weak so many things can contribute to getting the disease
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2
Q

What is low for many traits?

A

The contribution of individual allele to trait variation

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3
Q

What do GWAS do?

A

They only detect the genetics component of trait variation, not environmental

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4
Q

Comparative genomics

A

Rate of evolutionary change of each position across the genome

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5
Q

If we apply the comparative genomics method, what can we do?

A

Pinpoint sections that are genetically important

- higher chance of being functionally important (you would want to target these genes)

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6
Q

What do you need in for comparative genomics? (2)

A
  1. A lot of genome wide information (where polymorphism exists)
  2. Sequence information of many sequences from species
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7
Q

GERP

A

Genomic Evolutionary Rate Profiling

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8
Q

Genomic evolutionary rate profiling

A

Rates of change for each position across the genome

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9
Q

What does a high score of GERP mean?

A

Little change

- less important function because it is very conserved

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10
Q

What does a low score of GERP mean?

A

Lots of change

- functionally important

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11
Q

Where do most beta-thalassemia variants occur?

A

In small regions with high conservation

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12
Q

What does low rate of evolutionary change mean?

A

Functional important

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13
Q

What can low rate of evolutionary change be used to do?

A

Predict casual variants

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14
Q

What does GERP need? (2)

A
  1. Whole genome sequence information from many individuals

2. Closely related species

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15
Q

What are 2 types of functional data for prodicting impact of change?

A
  1. Promoter analysis
    - eg. known/predicted cis elements
  2. Protein sequence/structure analysis
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16
Q

What is promotor a model impact for?

A

Gene expression

17
Q

What is protein sequence/structure analysis a model impact for?

A

Change for each codon

18
Q

What does predicting impact on changes need? (4)

A
  1. Functional data on promoters
  2. Functional data on protein structures
  3. Whole genome sequence information from many individuals
  4. Closely related species
19
Q

What do whole genome association/ linkage studies do? (4)

A
  1. Look for associated loci
  2. Classify polymorphisms into functional classes
  3. Predict impact on candidate SNPs
  4. Narrows down candidates
20
Q

What are 2 problems with having too many associations?

A
  1. Missed/ weak associations
    - contribution might be too small
  2. Available markers to far way from casual differences for a given population
21
Q

What are 2 possible solutions for having too many associations?

A
  1. Increase population size

2. Increase number of markers

22
Q

What is an example of multiple genotyping approaches?

A

NGS

23
Q

NGS

A

Next generation sequencing

24
Q

Human genome project

A

Sequenced the complete human genome

25
Q

What are 4 components you get from the whole genome sequencing?

A
  1. Association genetics
  2. Genome structure
  3. Comparative genomics
  4. Medical genomics
26
Q

Association genetics (3)

A
  1. Polymorphism discovery
    - basis for whole genome association studies
  2. Allows jump from genetic to physical map
    - candidate genes
  3. Now polymorphism analysis
27
Q

Genome structure (2)

A
  1. Frequency and distribution of genes, repetitive elements, viral integrations, etc…
  2. Whole genome duplications
28
Q

Comparative genomics (2)

A
  1. Evolution of genes and gene families
  2. Loss and gain of genes on a global scale
    - how did the new gens and functions evolve
29
Q

Medical genomics (3)

A
  1. Predict/prevent disease
  2. Disease diagnosis
  3. Individualized treatment and medicine
    - eg) pharmacogenomics
30
Q

What is the genomic size of mRNA?

A

2,500bp

31
Q

What is the genomic size of gene size?

A

20,000bp

32
Q

What is the genomic size of E.coli?

A

5,000,000bp (5,000 genes)

Bio 361 - Molecular Genome and Genomics (35 decks)

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